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- PDB-3wf7: Crystal structure of S6K1 kinase domain in complex with a purine ... -

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Basic information

Entry
Database: PDB / ID: 3wf7
TitleCrystal structure of S6K1 kinase domain in complex with a purine derivative 1-(9H-purin-6-yl)-N-[3-(trifluoromethyl)phenyl]piperidine-4-carboxamide
ComponentsRibosomal protein S6 kinase beta-1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / SERINE/THREONINE PROTEIN KINASE DOMAIN / TRANSFERASE / PHOSPHORYLATION / ATP-BINDING / ZINC-BINDING / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


long-chain fatty acid import into cell / response to electrical stimulus involved in regulation of muscle adaptation / response to methamphetamine hydrochloride / skeletal muscle atrophy / regulation of D-glucose import / positive regulation of skeletal muscle tissue growth / negative regulation of TORC2 signaling / response to L-leucine / cellular response to nutrient / TORC1 signaling ...long-chain fatty acid import into cell / response to electrical stimulus involved in regulation of muscle adaptation / response to methamphetamine hydrochloride / skeletal muscle atrophy / regulation of D-glucose import / positive regulation of skeletal muscle tissue growth / negative regulation of TORC2 signaling / response to L-leucine / cellular response to nutrient / TORC1 signaling / response to glucagon / positive regulation of smooth muscle cell migration / phosphatidylinositol-mediated signaling / response to testosterone / germ cell development / TOR signaling / mTORC1-mediated signalling / positive regulation of translational initiation / response to tumor necrosis factor / long-term memory / behavioral fear response / skeletal muscle contraction / response to glucose / response to mechanical stimulus / positive regulation of TORC1 signaling / negative regulation of insulin receptor signaling pathway / protein serine/threonine/tyrosine kinase activity / positive regulation of mitotic cell cycle / cellular response to dexamethasone stimulus / peptide binding / protein phosphatase 2A binding / positive regulation of translation / negative regulation of extrinsic apoptotic signaling pathway / PDZ domain binding / positive regulation of smooth muscle cell proliferation / modulation of chemical synaptic transmission / response to nutrient levels / cellular response to growth factor stimulus / cellular response to type II interferon / G1/S transition of mitotic cell cycle / cellular response to insulin stimulus / response to toxic substance / cell migration / peptidyl-serine phosphorylation / response to lipopolysaccharide / response to ethanol / mitochondrial outer membrane / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / postsynapse / protein kinase activity / neuron projection / response to xenobiotic stimulus / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / negative regulation of apoptotic process / perinuclear region of cytoplasm / glutamatergic synapse / cell surface / signal transduction / mitochondrion / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein S6 kinase / Protein kinase, C-terminal / Protein kinase C terminal domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 ...Ribosomal protein S6 kinase / Protein kinase, C-terminal / Protein kinase C terminal domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-FS9 / Ribosomal protein S6 kinase beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsNiwa, H. / Shirouzu, M. / Yokoyama, S.
CitationJournal: J.Struct.Funct.Genom. / Year: 2014
Title: Crystal structures of the S6K1 kinase domain in complexes with inhibitors
Authors: Niwa, H. / Mikuni, J. / Sasaki, S. / Tomabechi, Y. / Honda, K. / Ikeda, M. / Ohsawa, N. / Wakiyama, M. / Handa, N. / Shirouzu, M. / Honma, T. / Tanaka, A. / Yokoyama, S.
History
DepositionJul 17, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Oct 29, 2014Group: Database references
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribosomal protein S6 kinase beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7274
Polymers37,1791
Non-polymers5483
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.438, 69.438, 145.649
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Ribosomal protein S6 kinase beta-1 / S6K-beta-1 / S6K1 / 70 kDa ribosomal protein S6 kinase 1 / Ribosomal protein S6 kinase I / ...S6K-beta-1 / S6K1 / 70 kDa ribosomal protein S6 kinase 1 / Ribosomal protein S6 kinase I / Serine/threonine-protein kinase 14A / p70 ribosomal S6 kinase alpha


Mass: 37178.816 Da / Num. of mol.: 1 / Fragment: UNP residues 78-399
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS6KB1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P23443, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FS9 / 1-(9H-purin-6-yl)-N-[3-(trifluoromethyl)phenyl]piperidine-4-carboxamide


Mass: 390.362 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H17F3N6O
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl, 3.7-3.9M sodium formate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 16, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 31350 / Num. obs: 31350 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Rsym value: 0.08 / Net I/σ(I): 26.3
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 1539 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→49.1 Å / SU ML: 0.22 / σ(F): 1.17 / Phase error: 21.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2919 5.02 %RANDOM
Rwork0.1731 31266 --
obs0.1755 31266 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.22 Å2 / Biso mean: 43.3488 Å2 / Biso min: 18.11 Å2
Refinement stepCycle: LAST / Resolution: 1.85→49.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2300 0 35 226 2561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072399
X-RAY DIFFRACTIONf_angle_d0.9673235
X-RAY DIFFRACTIONf_chiral_restr0.041346
X-RAY DIFFRACTIONf_plane_restr0.005408
X-RAY DIFFRACTIONf_dihedral_angle_d16.948919
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8497-1.880.32871290.300426372766
1.88-1.91240.27311480.272726152763
1.9124-1.94720.27961470.24525902737
1.9472-1.98470.31011480.234726622810
1.9847-2.02520.23221380.219326002738
2.0252-2.06920.25041040.205726852789
2.0692-2.11740.22071650.196425942759
2.1174-2.17030.22471310.181226622793
2.1703-2.2290.22351220.181726222744
2.229-2.29460.22751640.176625852749
2.2946-2.36860.21461290.17126392768
2.3686-2.45330.20381670.168526082775
2.4533-2.55150.22941420.177626142756
2.5515-2.66760.24681480.17726352783
2.6676-2.80830.19361410.17426182759
2.8083-2.98420.23181630.183626172780
2.9842-3.21460.28341270.187326292756
3.2146-3.5380.22661290.168626312760
3.538-4.04970.20021250.133926522777
4.0497-5.10140.17751390.138826142753
5.1014-49.11740.24581130.182326662779
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.177-0.39090.64273.97941.06943.83260.06490.57510.2762-0.6938-0.12070.0304-0.68670.04430.05080.32850.02140.00780.33940.03060.24314.3748-5.95659.7449
22.6341-1.0057-1.1172.190.97535.1860.0051-0.06850.1817-0.0314-0.0215-0.0173-0.01450.15150.04620.215-0.0199-0.03270.1529-0.04980.201215.0202-27.86923.2354
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 83:179 )
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 180:374 )

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